<div dir="ltr">On Thu, Feb 6, 2014 at 1:26 PM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div class="im"><span style="color:rgb(34,34,34)">A final note: in my experience, if you deposit a file containing hydrogens to the PDB, they're just going to delete them for you (whether you want this or not!), so it is not necessary to do any additional preparation. �In fact, I just did this last week, so we'll see what happens.</span></div>
</div></blockquote><div><br></div><div>In confirmation of this, here's what the PDB annotator said:</div><div><br></div><div>"The H atoms in the coordinates all have zero occupancy, would you like to remove them from the coordinates?"</div>
<div><br></div><div>Which obviously indicates a bug in phenix.refine (specifically the mmCIF output - the PDB-format file is okay), but my point stands.</div><div><br></div><div>-Nat</div></div></div></div>